Understanding key genetic make-up of different coat colour in Bayinbuluke sheep through a comparative transcriptome profiling analysis

Zhang, Lihua; Zhang, Xuemei; Long, Liang Qi; He, Shikun

doi:10.1016/j.smallrumres.2023.107028

Cited by 3 publications

(2 citation statements)

References 37 publications

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“…Focal adhesion assembly (GO:0048041) is a specialized structure that connects the cell cytoskeleton to the extracellular matrix [92]; focal adhesion (oas04510) plays a key role in the interaction between the extracellular matrix and pigment cells [92], which affects the development and distribution of pigment cells [93]. TERMS and PATHWAYS associated with neurotransmitters and their receptors may affect pigment synthesis and release [94], excitatory postsynaptic potential (GO:0060079) [94], glutamatergic synapse (GO:0098978) [94,95], dendritic spine (GO:0043197) [77,96,97], axon (GO:0030424) [98], postsynaptic membrane (GO:0045211) [99,100], integral component of postsynaptic density membrane (GO:0099061), axon guidance (oas04360), dopaminergic synapse (oas04728) [94,101], neuroactive ligand-receptor interaction (oas04080) [23], glutamatergic synapse (oas04724) [94,95], and long-term potentiation (oas04720) [100]. The histone deacetylase complex (GO:0000118) plays a key role in melanocyte development [102].…”

Section: Go Terms and Pathways Associated With Non-white Woolmentioning

confidence: 99%

“…With the improvement in sequencing technology and the development of in vitro breeding techniques, more and more genes with their variant forms have been discovered and their roles have been determined [9,21]. Currently, technologies such as whole genome sequencing, RNA sequencing, and gene editing techniques are widely used to mine and study wool color genes in sheep [16,17,22,23]. The wool color of sheep is controlled by a series of genes.…”

Section: Introductionmentioning

confidence: 99%

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Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Zhang,

Jin,

et al. 2023

Animals

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Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.

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Section: Go Terms and Pathways Associated With Non-white Woolmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Zhang,

Jin,

et al. 2023

Animals

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Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

Zhang,

Luosang,

Yuan

et al. 2024

BMC Genomics

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Background Gangba sheep as a famous breed of Tibetan sheep, its wool color is mainly white and black. Gangba wool is economically important as a high-quality raw material for Tibetan blankets and Tibetan serge. However, relatively few studies have been conducted on the wool color of Tibetan sheep. Results To fill this research gap, this study conducted an in-depth analysis of two populations of Gangba sheep (black and white wool color) using whole genome resequencing to identify genetic variation associated with wool color. Utilizing PCA, Genetic Admixture, and N-J Tree analyses, the present study revealed a consistent genetic relationship and structure between black and white wool colored Gangba sheep populations, which is consistent with their breed history. Analysis of selection signatures using multiple methods (FST, π ratio, Tajima's D), 370 candidate genes were screened in the black wool group (GBB vs GBW); among them, MC1R, MLPH, SPIRE2, RAB17, SMARCA4, IRF4, CAV1, USP7, TP53, MYO6, MITF, MC2R, TET2, NF1, JAK1, GABRR1 genes are mainly associated with melanin synthesis, melanin delivery, and distribution. The enrichment results of the candidate genes identified 35 GO entries and 19 KEGG pathways associated with the formation of the black phenotype. 311 candidate genes were screened in the white wool group (GBW vs GBB); among them, REST, POU2F1, ADCY10, CCNB1, EP300, BRD4, GLI3, and SDHA genes were mainly associated with interfering with the differentiation of neural crest cells into melanocytes, affecting the proliferation of melanocytes, and inhibiting melanin synthesis. 31 GO entries and 22 KEGG pathways were associated with the formation of the white phenotype. Conclusions This study provides important information for understanding the genetic mechanism of wool color in Gangba, and provides genetic knowledge for improving and optimizing the wool color of Tibetan sheep. Genetic improvement and selective breeding to produce wool of specific colors can meet the demand for a diversity of wool products in the Tibetan wool textile market.

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Transcriptomic and Metabolomic Analyses Reveal Molecular Regulatory Networks for Pigmentation Deposition in Sheep

Zhang,

Xu,

Chen

et al. 2024

IJMS

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Domestic animals have multiple phenotypes of skin and coat color, which arise from different genes and their products, such as proteins and metabolites responsible with melanin deposition. However, the complex regulatory network of melanin synthesis remains to be fully unraveled. Here, the skin and tongue tissues of Liangshan black sheep (black group) and Liangshan semi-fine-wool sheep (pink group) were collected, stained with hematoxylin–eosin (HE) and Masson–Fontana, and the transcriptomic and metabolomic data were further analyzed. We found a large deposit of melanin granules in the epidermis of the black skin and tongue. Transcriptome and metabolome analysis identified 744 differentially expressed genes (DEGs) and 443 differentially expressed metabolites (DEMs) between the pink and black groups. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed the DEGs and DEMs were mainly enriched in the pathways of secondary metabolic processes, melanin biosynthesis processes, melanin metabolism processes, melanosome membranes, pigment granule membranes, melanosome, tyrosine metabolism, and melanogenesis. Notably, we revealed the gene ENSARG00020006042 may be a family member of YWHAs and involved in regulating melanin deposition. Furthermore, several essential genes (TYR, TYRP1, DCT, PMEL, MLANA, SLC45A2) were significantly associated with metabolite prostaglandins and compounds involved in sheep pigmentation. These findings provide new evidence of the strong correlation between prostaglandins and related compounds and key genes that regulate sheep melanin synthesis, furthering our understanding of the regulatory mechanisms and molecular breeding of pigmentation in sheep.

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Understanding key genetic make-up of different coat colour in Bayinbuluke sheep through a comparative transcriptome profiling analysis

Cited by 3 publications

References 37 publications

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

Transcriptomic and Metabolomic Analyses Reveal Molecular Regulatory Networks for Pigmentation Deposition in Sheep

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